GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Dyella japonica UNC79MFTsu3.2

Align Acetylglutamate kinase; EC 2.7.2.8 (characterized, see rationale)
to candidate N515DRAFT_3768 N515DRAFT_3768 N-acetylglutamate kinase

Query= uniprot:A0A1I2DIM7
         (438 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3768
          Length = 438

 Score =  860 bits (2221), Expect = 0.0
 Identities = 438/438 (100%), Positives = 438/438 (100%)

Query: 1   MEAHKHTRKTIVRLLSSMGSAKEIQQYLKRFSQLDAKRFAVVKVGGAVLRDDLPALTSSL 60
           MEAHKHTRKTIVRLLSSMGSAKEIQQYLKRFSQLDAKRFAVVKVGGAVLRDDLPALTSSL
Sbjct: 1   MEAHKHTRKTIVRLLSSMGSAKEIQQYLKRFSQLDAKRFAVVKVGGAVLRDDLPALTSSL 60

Query: 61  TFLQQVGLTPIVLHGAGPQLDEELSAAGIQKQTVNGLRVTSPKALAIVRKVFQEQNLRLV 120
           TFLQQVGLTPIVLHGAGPQLDEELSAAGIQKQTVNGLRVTSPKALAIVRKVFQEQNLRLV
Sbjct: 61  TFLQQVGLTPIVLHGAGPQLDEELSAAGIQKQTVNGLRVTSPKALAIVRKVFQEQNLRLV 120

Query: 121 EALQGMDTRATSVPSGVFTSEYLDRDVYGLVGKVSSINLAPIEASLRAGSIPVIASLGET 180
           EALQGMDTRATSVPSGVFTSEYLDRDVYGLVGKVSSINLAPIEASLRAGSIPVIASLGET
Sbjct: 121 EALQGMDTRATSVPSGVFTSEYLDRDVYGLVGKVSSINLAPIEASLRAGSIPVIASLGET 180

Query: 181 AEGQILNINADFAANELVRVLQPYKIVFLTGTGGLLDDKGRIIDSINLSTEYEHLMAQPW 240
           AEGQILNINADFAANELVRVLQPYKIVFLTGTGGLLDDKGRIIDSINLSTEYEHLMAQPW
Sbjct: 181 AEGQILNINADFAANELVRVLQPYKIVFLTGTGGLLDDKGRIIDSINLSTEYEHLMAQPW 240

Query: 241 INGGMRVKIEQIADLLSSLPLTSSVSITQPSELAKELFTHKGSGTLVRRGEKVLRYESWE 300
           INGGMRVKIEQIADLLSSLPLTSSVSITQPSELAKELFTHKGSGTLVRRGEKVLRYESWE
Sbjct: 241 INGGMRVKIEQIADLLSSLPLTSSVSITQPSELAKELFTHKGSGTLVRRGEKVLRYESWE 300

Query: 301 GIDLARMRELIESSFGRKVVADYFERTRPYRIYVSENYRAAMILTQEEGLAYLDKFAVLD 360
           GIDLARMRELIESSFGRKVVADYFERTRPYRIYVSENYRAAMILTQEEGLAYLDKFAVLD
Sbjct: 301 GIDLARMRELIESSFGRKVVADYFERTRPYRIYVSENYRAAMILTQEEGLAYLDKFAVLD 360

Query: 361 DAQGEGLGRAVWQVMREENPQLFWRSRHGNQVNIFYYAESDGCFKQERWKVFWYGLKNFG 420
           DAQGEGLGRAVWQVMREENPQLFWRSRHGNQVNIFYYAESDGCFKQERWKVFWYGLKNFG
Sbjct: 361 DAQGEGLGRAVWQVMREENPQLFWRSRHGNQVNIFYYAESDGCFKQERWKVFWYGLKNFG 420

Query: 421 EIERCVAHCAVRPATLMD 438
           EIERCVAHCAVRPATLMD
Sbjct: 421 EIERCVAHCAVRPATLMD 438


Lambda     K      H
   0.319    0.135    0.389 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 712
Number of extensions: 16
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 438
Length of database: 438
Length adjustment: 32
Effective length of query: 406
Effective length of database: 406
Effective search space:   164836
Effective search space used:   164836
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory